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R/data.R
In aquacultuR: A Comprehensive R Tool for Zootechnical Metrics
#' Treatments
#'
#' This dataset contains the rearing tank and respective treatment assigned to
#' it. It represents the metadata from a feeding trial with Atlantic salmon
#' (Salmo salar). The related dataset was published by Liland et al. (2024)
#' and is from the first out of two trials ("Trial A").
#'
#' @format A tibble with nine rows and two columns:
#' \describe{
#' \item{tank}{factor; rearing tank identifier.}
#' \item{treatment}{factor; treatment identifier.}
#' }
#'
#' @examples
#' treatments
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name treatments
NULL
#' Daily water parameters
#'
#' This dataset contains daily readings of water temperature, salinity, and
#' dissolved oxygen from a feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ("WaterParametersDaily") was published by
#' Liland et al. (2024) and is from the first out of two trials
#' ("Trial A"). Alterations to the original data structure were done by
#' 1) converting the double-row column names into single-row column names,
#' 2) shortening the column names, and 3) converting the table into long
#' format by moving the tank IDs into a separate column.
#'
#' @format A tibble with 270 rows and 6 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{temp}{numeric; water temperature in degrees Celsius.}
#' \item{salinity}{numeric; salinity in parts per thousand.}
#' \item{do_perc}{numeric; dissolved oxygen in percentage saturation.}
#' \item{do_conc}{numeric; dissolved oxygen concentration in mg/L.}
#' }
#'
#' @examples
#' water_params
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name water_params
NULL
#' Daily feed intake
#'
#' This dataset contains daily feed intake data from a feeding trial with
#' Atlantic salmon (Salmo salar).
#' The original dataset ("FeedIntake") was published by Liland et al. (2024)
#' and is from the first out of two trials ("Trial A"). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, 2) shortening the column names, and 3)
#' converting the table into long format by moving the tank IDs into a separate
#' column. NA values have been replaced by the recalculated feed intakes for
#' the respective day.
#'
#' @format A tibble with 270 rows and 4 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{daily_feed_intake}{numeric; daily feed intake in gram per fish.}
#' \item{cumulative_feed_intake}{numeric; cumulatic feed intake in gram per
#' fish.}
#' }
#'
#' @examples
#' feed_intake
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name feed_intake
NULL
#' Sampling data
#'
#' This dataset contains the fish weight, fork length, sex, liver weight,
#' hepatosomatic index, heart weight, cardiosomatic index, gonad weight,
#' gonadosomatic index, viscera weight, and viscerosomatic index from a
#' feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ('FeedIntake') was published by Liland et al. (2024)
#' and is from the first out of two trials ('Trial A'). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, and 2) removing the 'sex' column.
#'
#' @format A tibble with 181 rows and 14 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{replicate}{factor; replicate identifier.}
#' \item{sample_type}{factor; type of sample.}
#' \item{fish_weight}{numeric; weight of fish in gram.}
#' \item{fork_length}{numeric; length of fish from the tip of the snout to the
#' end of the middle caudal fin rays in centimeter.}
#' \item{liver_weight}{numeric; weight of the liver in gram.}
#' \item{hsi}{numeric; hepatosomatic index in percent.}
#' \item{heart_weight}{numeric; weight of the heart in gram.}
#' \item{csi}{numeric; cardiosomatic index in percent.}
#' \item{gonad_weight}{numeric; weight of the gonads in gram.}
#' \item{gsi}{numeric; gonadosomatic index in percent.}
#' \item{viscera_weight}{numeric; weight of the viscera in gram.}
#' \item{vsi}{numeric; viscerosomatic index in percent.}
#' }
#'
#' @examples
#' samplings
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name samplings
NULL
#' Daily count of live and dead fish
#'
#' This dataset contains the daily count of dead and alive fish during a 29-day
#' feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ('NumberOfFish') was published by Liland et al. (2024)
#' and is from the first out of two trials ('Trial A'). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, 2) shortening the column names, and 3)
#' converting the table into long format by moving the tank IDs into a separate
#' column.
#'
#' @format A tibble with 270 rows and 4 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{total_number}{numeric; count of fish stocked at the beginning of the
#' experiment.}
#' \item{dead}{numeric; count of dead fish on each recorded day of the
#' experiment.}
#' }
#'
#' @examples
#' fishcount
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name fishcount
NULL
#' Fish body composition
#'
#' This dataset contains compositional data on the proximate composition and
#' some key minerals in the body of Atlantic salmon (Salmo salar) at the
#' beginning and the end of a trial.
#' The original dataset ('BodyComposition_tank') was published by Liland et al.
#' (2024) and is from the first out of two trials ('Trial A'). Alterations to
#' the original data structure were done by 1) converting the double-row column
#' names into single-row column names and 2) removing the 'sex' column.
#'
#' @format A tibble with 12 rows and 14 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{treatment}{factor; treatment identifier.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{dm}{numeric; dry matter content of fish tissue in g/g.}
#' \item{water}{numeric; content of fish tissue in g/g.}
#' \item{ash}{numeric; content of fish tissue in g/g on dry matter
#' basis.}
#' \item{energy}{numeric; gross energy content of fish tissue in kJ/g on dry
#' matter basis.}
#' \item{fat}{numeric; crude fat content of fish tissue in g/g on dry
#' matter basis.}
#' \item{protein}{numeric; crude protein content of fish tissue in g/g on
#' dry matter basis.}
#' \item{ca}{numeric; calcium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{k}{numeric; potassium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{mg}{numeric; magnesium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{na}{numeric; sodium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{phosphorus}{numeric; content of fish tissue in mg/kg on dry matter
#' basis.}
#' }
#'
#' @examples
#' bodycomp
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name bodycomp
NULL
#' Feed composition
#'
#' This dataset contains compositional data of Skretting Protec, a commercial
#' fish feed. The data comprises the proximate composition, phosphorus, and
#' some essential amino acids.
#'
#' @format A tibble with one row and 25 columns:
#' \describe{
#' \item{diet}{character; feed name.}
#' \item{dry_matter}{numeric; content of feed in g/g.}
#' \item{crude_protein}{numeric; content of feed in g/g as fed.}
#' \item{crude_lipids}{numeric; content of feed in g/g as fed.}
#' \item{ash}{numeric; content of feed in g/g as fed.}
#' \item{gross_energy}{numeric; content of feed in MJ per kg as fed.}
#' \item{phosphorus}{numeric; content of feed in g/g as fed.}
#' \item{arginine}{numeric; content of feed in g/g as fed.}
#' \item{histidine}{numeric; content of feed in g/g as fed.}
#' \item{isoleucine}{numeric; content of feed in g/g as fed.}
#' \item{leucine}{numeric; content of feed in g/g as fed.}
#' \item{lysine}{numeric; content of feed in g/g as fed.}
#' \item{threonine}{numeric; content of feed in g/g as fed.}
#' \item{tryptophan}{numeric; content of feed in g/g as fed.}
#' \item{valine}{numeric; content of feed in g/g as fed.}
#' \item{methionine}{numeric; content of feed in g/g as fed.}
#' \item{cysteine}{numeric; content of feed in g/g as fed.}
#' \item{phenylalanine}{numeric; content of feed in g/g as fed.}
#' \item{tyrosine}{numeric; content of feed in g/g as fed.}
#' \item{aspartic_acid}{numeric; content of feed in g/g as fed.}
#' \item{glutamic_acid}{numeric; content of feed in g/g as fed.}
#' \item{alanine}{numeric; content of feed in g/g as fed.}
#' \item{glycine}{numeric; content of feed in g/g as fed.}
#' \item{proline}{numeric; content of feed in g/g as fed.}
#' \item{serine}{numeric; content of feed in g/g as fed.}
#' }
#'
#' @examples
#' feedcomp
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name feedcomp
NULL
#' Digestibility of dry matter
#'
#' This dataset contains example data to calculate the apparent digestibility
#' of two diets that differ in their dry matter mass fraction and in the mass
#' fraction of digestibility markers in the feces.
#'
#' @format A tibble with two rows and four columns:
#' \describe{
#' \item{diet}{character; feed identifier.}
#' \item{dm}{numeric; mass fraction of dry matter in the feed. Data reported
#' as value between 0 and 1, corresponding to g/g.}
#' \item{std_feed}{numeric; mass fraction of digestibility marker in feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{std_feces}{numeric; mass fraction of digestibility marker in feces.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestdm
#'
#' @docType data
#' @keywords datasets
#' @name digestdm
NULL
#' Digestibility of feed nutrients
#'
#' This dataset contains example data for the calculation of apparent
#' digestibility coefficients for the digestibility of nitrogen in the dry
#' matter fraction of an aquaculture feed.
#'
#' @format A tibble with two rows and six columns:
#' \describe{
#' \item{diet}{character; feed identifier.}
#' \item{dm}{numeric; mass fraction of dry matter in the feed. Data reported
#' as value between 0 and 1, corresponding to g/g.}
#' \item{N_feed}{numeric; mass fraction of nitrogen in feed. Data reported as
#' value between 0 and 1, corresponding to g/g.}
#' \item{std_feed}{numeric; mass fraction of digestibility marker in feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{N_feces}{numeric; mass fraction of nitrogen in feces in g/kg.}
#' \item{std_feces}{numeric; mass fraction of digestibility marker in feces.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestnut
#'
#' @docType data
#' @keywords dataset
#' @name digestnut
NULL
#' Digestibility of a feed ingredient
#'
#' This dataset contains example data for the determination of the apparent
#' digestibility of feed ingredients by using a reference diet and replacing
#' a part (usually 30%) of it by the feed ingredient to be evaluated.
#' The dataset is based on Bureau et al. (1999) but was presented in its
#' complete form in Bureau & Hua (2006).
#'
#' @format A tibble with one row and eight columns
#' \describe{
#' \item{diet_reference}{character; reference feed identifier.}
#' \item{ingredient}{character; feed ingredient identifier.}
#' \item{adc_reference}{numeric; apparent digestibility coefficient of the
#' reference feed. The data is a value between 0 and 1.}
#' \item{adc_test}{numeric; apparent digestibility coefficient of the test
#' feed. The data is a value between 0 and 1.}
#' \item{dm_reference}{numeric; mass fraction of dry matter in the reference feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{dm_ingr}{numeric; mass fraction of dry matter in the feed ingredient.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{CP_reference}{numeric; mass fraction of crude protein in the pelleted
#' reference feed reported as value between 0 and 1, corresponding to g/g.}
#' \item{CP_ingr}{numeric; mass fraction of crude protein in the feed
#' ingredient. Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestingr
#'
#' @references Bureau, D. P. & Hua, K. (2006). Letter to the Editor of
#' Aquaculture. Aquaculture, 252(2-4), 103–105.
#' https://doi.org/10.1016/j.aquaculture.2006.01.028
#' @references Bureau, D. P., Harris, A. M. & Cho, C. Y. (1999). Apparent
#' digestibility of rendered animal protein ingredients for rainbow trout
#' (Oncorhynchus mykiss). Aquaculture, 180, 345–358.
#' https://doi.org/10.1016/S0044-8486(99)00210-0
#'
#' @docType data
#' @keywords dataset
#' @name digestingr
NULL
#' Fish biomass and bodyweights from the first polyculture experiment
#'
#' A dataset containing fish weights from a polyculture experiment with
#' pikeperch (Sander lucioperca) and Russian sturgeon.
#'
#' @format A tibble with 24 rows and eight columns:
#' \describe{
#' \item{tank}{character; rearing tank identifier.}
#' \item{treat_id}{character; treatment identifier.}
#' \item{count_start}{numeric; fish count at the beginning of the experiment.}
#' \item{count_end}{numeric; fish count at the end of the experiment.}
#' \item{biomass_kg_start}{numeric; total fish biomass in kg at the beginning
#' of the experiment.}
#' \item{biomass_kg_end}{numeric; total fish biomass in kg at the end of the
#' experiment.}
#' }
#'
#' @examples
#' weight
#'
#' @docType data
#' @keywords datasets
#' @name weight
NULL
#' Individual fish bodyweights during a polyculture experiment
#'
#' A dataset holding weight data of tagged individuals of two different fish
#' species, pikeperch (Sander lucioperca) and largemouth bass (Micropterus
#' salmoides), at the beginning and the end of a polyculture experiment for
#' aquaculture purposes.
#'
#' @format A tibble with 396 rows and four columns:
#' \describe{
#' \item{species}{character; species identifier.}
#' \item{culture_sys}{character; culture system identifier.}
#' \item{ibw_g}{numeric; initial bodyweight in gram.}
#' \item{fbw_g}{numeric; final bodyweight in gram.}
#' }
#'
#' @examples
#' weight2
#'
#' @references Pěnka T., Malinovskyi O., Křišťan J., Imentai A., Policar T.
#' (2021): Effect of density and mixed culture with pikeperch (Sander
#' lucioperca) on effectivity of largemouth bass (Micropterus salmoides)
#' intensive culture. Czech Journal of Animal Science, 66: 428–440.
#'
#' @docType data
#' @keywords datasets
#' @name weight2
NULL
#' Rearing data from the first polyculture experiment
#'
#' A dataset containing feed quantities fed per tank and the average water
#' temperature over all tanks stocked with pikeperch oder sturgeon. The
#' variables are as follows:
#'
#' @format A data frame containing 24 rows and four columns:
#' \describe{
#' \item{tank}{character; unique identifier for each fish tank.}
#' \item{feed_g}{numeric; total feed input in gram over the duration of the
#' experiment.}
#' \item{temp_C}{numeric; average water temperature in degrees Celsius.}
#' \item{duration}{numeric; total duration of the experiment in days.}
#' }
#'
#' @examples
#' rearing
#'
#' @docType data
#' @keywords datasets
#' @name rearing
NULL
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#' Treatments
#'
#' This dataset contains the rearing tank and respective treatment assigned to
#' it. It represents the metadata from a feeding trial with Atlantic salmon
#' (Salmo salar). The related dataset was published by Liland et al. (2024)
#' and is from the first out of two trials ("Trial A").
#'
#' @format A tibble with nine rows and two columns:
#' \describe{
#' \item{tank}{factor; rearing tank identifier.}
#' \item{treatment}{factor; treatment identifier.}
#' }
#'
#' @examples
#' treatments
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name treatments
NULL
#' Daily water parameters
#'
#' This dataset contains daily readings of water temperature, salinity, and
#' dissolved oxygen from a feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ("WaterParametersDaily") was published by
#' Liland et al. (2024) and is from the first out of two trials
#' ("Trial A"). Alterations to the original data structure were done by
#' 1) converting the double-row column names into single-row column names,
#' 2) shortening the column names, and 3) converting the table into long
#' format by moving the tank IDs into a separate column.
#'
#' @format A tibble with 270 rows and 6 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{temp}{numeric; water temperature in degrees Celsius.}
#' \item{salinity}{numeric; salinity in parts per thousand.}
#' \item{do_perc}{numeric; dissolved oxygen in percentage saturation.}
#' \item{do_conc}{numeric; dissolved oxygen concentration in mg/L.}
#' }
#'
#' @examples
#' water_params
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name water_params
NULL
#' Daily feed intake
#'
#' This dataset contains daily feed intake data from a feeding trial with
#' Atlantic salmon (Salmo salar).
#' The original dataset ("FeedIntake") was published by Liland et al. (2024)
#' and is from the first out of two trials ("Trial A"). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, 2) shortening the column names, and 3)
#' converting the table into long format by moving the tank IDs into a separate
#' column. NA values have been replaced by the recalculated feed intakes for
#' the respective day.
#'
#' @format A tibble with 270 rows and 4 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{daily_feed_intake}{numeric; daily feed intake in gram per fish.}
#' \item{cumulative_feed_intake}{numeric; cumulatic feed intake in gram per
#' fish.}
#' }
#'
#' @examples
#' feed_intake
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name feed_intake
NULL
#' Sampling data
#'
#' This dataset contains the fish weight, fork length, sex, liver weight,
#' hepatosomatic index, heart weight, cardiosomatic index, gonad weight,
#' gonadosomatic index, viscera weight, and viscerosomatic index from a
#' feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ('FeedIntake') was published by Liland et al. (2024)
#' and is from the first out of two trials ('Trial A'). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, and 2) removing the 'sex' column.
#'
#' @format A tibble with 181 rows and 14 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{replicate}{factor; replicate identifier.}
#' \item{sample_type}{factor; type of sample.}
#' \item{fish_weight}{numeric; weight of fish in gram.}
#' \item{fork_length}{numeric; length of fish from the tip of the snout to the
#' end of the middle caudal fin rays in centimeter.}
#' \item{liver_weight}{numeric; weight of the liver in gram.}
#' \item{hsi}{numeric; hepatosomatic index in percent.}
#' \item{heart_weight}{numeric; weight of the heart in gram.}
#' \item{csi}{numeric; cardiosomatic index in percent.}
#' \item{gonad_weight}{numeric; weight of the gonads in gram.}
#' \item{gsi}{numeric; gonadosomatic index in percent.}
#' \item{viscera_weight}{numeric; weight of the viscera in gram.}
#' \item{vsi}{numeric; viscerosomatic index in percent.}
#' }
#'
#' @examples
#' samplings
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name samplings
NULL
#' Daily count of live and dead fish
#'
#' This dataset contains the daily count of dead and alive fish during a 29-day
#' feeding trial with Atlantic salmon (Salmo salar).
#' The original dataset ('NumberOfFish') was published by Liland et al. (2024)
#' and is from the first out of two trials ('Trial A'). Alterations to the
#' original data structure were done by 1) converting the double-row column
#' names into single-row column names, 2) shortening the column names, and 3)
#' converting the table into long format by moving the tank IDs into a separate
#' column.
#'
#' @format A tibble with 270 rows and 4 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{total_number}{numeric; count of fish stocked at the beginning of the
#' experiment.}
#' \item{dead}{numeric; count of dead fish on each recorded day of the
#' experiment.}
#' }
#'
#' @examples
#' fishcount
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name fishcount
NULL
#' Fish body composition
#'
#' This dataset contains compositional data on the proximate composition and
#' some key minerals in the body of Atlantic salmon (Salmo salar) at the
#' beginning and the end of a trial.
#' The original dataset ('BodyComposition_tank') was published by Liland et al.
#' (2024) and is from the first out of two trials ('Trial A'). Alterations to
#' the original data structure were done by 1) converting the double-row column
#' names into single-row column names and 2) removing the 'sex' column.
#'
#' @format A tibble with 12 rows and 14 columns:
#' \describe{
#' \item{date}{date; date of data recording.}
#' \item{treatment}{factor; treatment identifier.}
#' \item{tank}{factor; rearing tank identifier.}
#' \item{dm}{numeric; dry matter content of fish tissue in g/g.}
#' \item{water}{numeric; content of fish tissue in g/g.}
#' \item{ash}{numeric; content of fish tissue in g/g on dry matter
#' basis.}
#' \item{energy}{numeric; gross energy content of fish tissue in kJ/g on dry
#' matter basis.}
#' \item{fat}{numeric; crude fat content of fish tissue in g/g on dry
#' matter basis.}
#' \item{protein}{numeric; crude protein content of fish tissue in g/g on
#' dry matter basis.}
#' \item{ca}{numeric; calcium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{k}{numeric; potassium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{mg}{numeric; magnesium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{na}{numeric; sodium content of fish tissue in mg/kg on dry matter
#' basis.}
#' \item{phosphorus}{numeric; content of fish tissue in mg/kg on dry matter
#' basis.}
#' }
#'
#' @examples
#' bodycomp
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name bodycomp
NULL
#' Feed composition
#'
#' This dataset contains compositional data of Skretting Protec, a commercial
#' fish feed. The data comprises the proximate composition, phosphorus, and
#' some essential amino acids.
#'
#' @format A tibble with one row and 25 columns:
#' \describe{
#' \item{diet}{character; feed name.}
#' \item{dry_matter}{numeric; content of feed in g/g.}
#' \item{crude_protein}{numeric; content of feed in g/g as fed.}
#' \item{crude_lipids}{numeric; content of feed in g/g as fed.}
#' \item{ash}{numeric; content of feed in g/g as fed.}
#' \item{gross_energy}{numeric; content of feed in MJ per kg as fed.}
#' \item{phosphorus}{numeric; content of feed in g/g as fed.}
#' \item{arginine}{numeric; content of feed in g/g as fed.}
#' \item{histidine}{numeric; content of feed in g/g as fed.}
#' \item{isoleucine}{numeric; content of feed in g/g as fed.}
#' \item{leucine}{numeric; content of feed in g/g as fed.}
#' \item{lysine}{numeric; content of feed in g/g as fed.}
#' \item{threonine}{numeric; content of feed in g/g as fed.}
#' \item{tryptophan}{numeric; content of feed in g/g as fed.}
#' \item{valine}{numeric; content of feed in g/g as fed.}
#' \item{methionine}{numeric; content of feed in g/g as fed.}
#' \item{cysteine}{numeric; content of feed in g/g as fed.}
#' \item{phenylalanine}{numeric; content of feed in g/g as fed.}
#' \item{tyrosine}{numeric; content of feed in g/g as fed.}
#' \item{aspartic_acid}{numeric; content of feed in g/g as fed.}
#' \item{glutamic_acid}{numeric; content of feed in g/g as fed.}
#' \item{alanine}{numeric; content of feed in g/g as fed.}
#' \item{glycine}{numeric; content of feed in g/g as fed.}
#' \item{proline}{numeric; content of feed in g/g as fed.}
#' \item{serine}{numeric; content of feed in g/g as fed.}
#' }
#'
#' @examples
#' feedcomp
#'
#' @references Liland, N., Rønnestad, I., Azevedo, M., Lai, F., Oulie, F.,
#' Conceição, L., Soares, F. (2024): Dataset on the performance of Atlantic
#' salmon (Salmo salar) reared at different dissolved oxygen levels under
#' experimental conditions. Data in Brief 57, 110983.
#' https://doi.org/10.1016/j.dib.2024.110983
#'
#' @docType data
#' @keywords datasets
#' @name feedcomp
NULL
#' Digestibility of dry matter
#'
#' This dataset contains example data to calculate the apparent digestibility
#' of two diets that differ in their dry matter mass fraction and in the mass
#' fraction of digestibility markers in the feces.
#'
#' @format A tibble with two rows and four columns:
#' \describe{
#' \item{diet}{character; feed identifier.}
#' \item{dm}{numeric; mass fraction of dry matter in the feed. Data reported
#' as value between 0 and 1, corresponding to g/g.}
#' \item{std_feed}{numeric; mass fraction of digestibility marker in feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{std_feces}{numeric; mass fraction of digestibility marker in feces.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestdm
#'
#' @docType data
#' @keywords datasets
#' @name digestdm
NULL
#' Digestibility of feed nutrients
#'
#' This dataset contains example data for the calculation of apparent
#' digestibility coefficients for the digestibility of nitrogen in the dry
#' matter fraction of an aquaculture feed.
#'
#' @format A tibble with two rows and six columns:
#' \describe{
#' \item{diet}{character; feed identifier.}
#' \item{dm}{numeric; mass fraction of dry matter in the feed. Data reported
#' as value between 0 and 1, corresponding to g/g.}
#' \item{N_feed}{numeric; mass fraction of nitrogen in feed. Data reported as
#' value between 0 and 1, corresponding to g/g.}
#' \item{std_feed}{numeric; mass fraction of digestibility marker in feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{N_feces}{numeric; mass fraction of nitrogen in feces in g/kg.}
#' \item{std_feces}{numeric; mass fraction of digestibility marker in feces.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestnut
#'
#' @docType data
#' @keywords dataset
#' @name digestnut
NULL
#' Digestibility of a feed ingredient
#'
#' This dataset contains example data for the determination of the apparent
#' digestibility of feed ingredients by using a reference diet and replacing
#' a part (usually 30%) of it by the feed ingredient to be evaluated.
#' The dataset is based on Bureau et al. (1999) but was presented in its
#' complete form in Bureau & Hua (2006).
#'
#' @format A tibble with one row and eight columns
#' \describe{
#' \item{diet_reference}{character; reference feed identifier.}
#' \item{ingredient}{character; feed ingredient identifier.}
#' \item{adc_reference}{numeric; apparent digestibility coefficient of the
#' reference feed. The data is a value between 0 and 1.}
#' \item{adc_test}{numeric; apparent digestibility coefficient of the test
#' feed. The data is a value between 0 and 1.}
#' \item{dm_reference}{numeric; mass fraction of dry matter in the reference feed.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{dm_ingr}{numeric; mass fraction of dry matter in the feed ingredient.
#' Data reported as value between 0 and 1, corresponding to g/g.}
#' \item{CP_reference}{numeric; mass fraction of crude protein in the pelleted
#' reference feed reported as value between 0 and 1, corresponding to g/g.}
#' \item{CP_ingr}{numeric; mass fraction of crude protein in the feed
#' ingredient. Data reported as value between 0 and 1, corresponding to g/g.}
#' }
#'
#' @examples
#' digestingr
#'
#' @references Bureau, D. P. & Hua, K. (2006). Letter to the Editor of
#' Aquaculture. Aquaculture, 252(2-4), 103–105.
#' https://doi.org/10.1016/j.aquaculture.2006.01.028
#' @references Bureau, D. P., Harris, A. M. & Cho, C. Y. (1999). Apparent
#' digestibility of rendered animal protein ingredients for rainbow trout
#' (Oncorhynchus mykiss). Aquaculture, 180, 345–358.
#' https://doi.org/10.1016/S0044-8486(99)00210-0
#'
#' @docType data
#' @keywords dataset
#' @name digestingr
NULL
#' Fish biomass and bodyweights from the first polyculture experiment
#'
#' A dataset containing fish weights from a polyculture experiment with
#' pikeperch (Sander lucioperca) and Russian sturgeon.
#'
#' @format A tibble with 24 rows and eight columns:
#' \describe{
#' \item{tank}{character; rearing tank identifier.}
#' \item{treat_id}{character; treatment identifier.}
#' \item{count_start}{numeric; fish count at the beginning of the experiment.}
#' \item{count_end}{numeric; fish count at the end of the experiment.}
#' \item{biomass_kg_start}{numeric; total fish biomass in kg at the beginning
#' of the experiment.}
#' \item{biomass_kg_end}{numeric; total fish biomass in kg at the end of the
#' experiment.}
#' }
#'
#' @examples
#' weight
#'
#' @docType data
#' @keywords datasets
#' @name weight
NULL
#' Individual fish bodyweights during a polyculture experiment
#'
#' A dataset holding weight data of tagged individuals of two different fish
#' species, pikeperch (Sander lucioperca) and largemouth bass (Micropterus
#' salmoides), at the beginning and the end of a polyculture experiment for
#' aquaculture purposes.
#'
#' @format A tibble with 396 rows and four columns:
#' \describe{
#' \item{species}{character; species identifier.}
#' \item{culture_sys}{character; culture system identifier.}
#' \item{ibw_g}{numeric; initial bodyweight in gram.}
#' \item{fbw_g}{numeric; final bodyweight in gram.}
#' }
#'
#' @examples
#' weight2
#'
#' @references Pěnka T., Malinovskyi O., Křišťan J., Imentai A., Policar T.
#' (2021): Effect of density and mixed culture with pikeperch (Sander
#' lucioperca) on effectivity of largemouth bass (Micropterus salmoides)
#' intensive culture. Czech Journal of Animal Science, 66: 428–440.
#'
#' @docType data
#' @keywords datasets
#' @name weight2
NULL
#' Rearing data from the first polyculture experiment
#'
#' A dataset containing feed quantities fed per tank and the average water
#' temperature over all tanks stocked with pikeperch oder sturgeon. The
#' variables are as follows:
#'
#' @format A data frame containing 24 rows and four columns:
#' \describe{
#' \item{tank}{character; unique identifier for each fish tank.}
#' \item{feed_g}{numeric; total feed input in gram over the duration of the
#' experiment.}
#' \item{temp_C}{numeric; average water temperature in degrees Celsius.}
#' \item{duration}{numeric; total duration of the experiment in days.}
#' }
#'
#' @examples
#' rearing
#'
#' @docType data
#' @keywords datasets
#' @name rearing
NULL
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